Dear Galaxy
When running HiSeq shot metagenomics sample from the
environment against megablast and taxonomic
representation, How do I filter/remove all the 16s and
other conserved sequences.
The problem if blasting a single organism that has a
fraction of conserved sequence, the results will align
with E.coli 10,000 times more then the possible target
organism. This data would be wrong and misleading. For
example a 100mg sample that was negative for e coli
using MUG test, give thousands of hits with galaxy.
1) Is there a "filter conserved sequences" setting?
2) Is there a "remove model organisms" setting?
Scott Tighe
--Core Laboratory Research Staff
Advanced Genome Technologies Core
Deep Sequencing (MPS) Facility
Vermont Cancer Center
149 Beaumont Ave
University of Vermont HSRF 303
Burlington Vermont USA 05045
802-656-AGTC
802-999-6666 (cell)
Quoting Jennifer Jackson <
jen@bx.psu.edu>:
> Hello Elwood,
>
> Are you still having connection issues today? Or
is this resolved?
>
> Best,
>
> Jen
> Galaxy team
>
> On 9/13/13 11:36 AM, Elwood Linney wrote:
>> A message sent earlier this week by me
indicated that I could not connect to Galaxy via Fetch
to download data.
>>
>> A reply indicated a glitch was fixed.
>>
>> I then could connect with Fetch and I tried
to transfer 4 x 16gb files and the connection
disconnected about 4 times.
>>
>> Now, once again, I cannot connect with Galaxy
online to transfer data.
>>
>> Is this a problem that can be solved-either
at my end or at Galaxy?
>>
>> Elwood Linney
>>
>>
>>
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>
> --Jennifer Hillman-Jackson
>
http://galaxyproject.org
___________________________________________________________
The Galaxy User list should be used for the discussion
of
Galaxy analysis and other features on the public
server
at usegalaxy.org. Please keep all replies on the list
by
using "reply all" in your mail client. For discussion
of
local Galaxy instances and the Galaxy source code,
please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy
lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search
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